Basic tutorials

import packages and load data

[1]:

import Polyomino as plmo

[2]:

import scanpy as sc

[3]:

scdata = sc.read_h5ad('./data/Figure2/proportion_simulated/Scenario1.h5ad')

[4]:

stdata = sc.read_h5ad('./data/Figure2/proportion_simulated/Eng2019_seqFISH.h5ad')

generate grids

[5]:

stdata_grid = plmo.generate_grid(stdata,width=500)

set up Polyomino object and running

[10]:

plmo_object = plmo.Polyomino(scdata,stdata_grid,cluster_time=1,device='cpu')

[11]:

plmo_object.allocate()

Running 1-th clustering.
Running 1-th mapping.
Total loss: -1.820
Total loss: -1.958
Total loss: -1.958
Total loss: -1.958
Total loss: -1.958
Starting spot mapping.
Total loss: -1.886
Total loss: -1.958
Total loss: -1.959
Total loss: -1.959
Total loss: -1.959
Spot mapping completed.
Mapping matrix saved in zm.spot_matrix

allocating single cell to spatial locations

[13]:

cell_alocated_data = plmo.sc2sc(scdata, stdata, plmo_object.spot_matrix,thres=0.1,method='max')

100%|██████████| 68/68 [00:01<00:00, 54.82it/s]

[14]:

sc.pl.spatial(cell_alocated_data,color='celltype',spot_size=120)

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